biostudies-arrayexpressNils Jonathan TrostHomo sapiensCellranger-atac (1.1.0)ArchR (1.0.2), MACS2 (2.1.2), chromVar (1.20.2)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15028This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 22,032 nuclei in the developing human female and male gonads across several timepoints during prenatal development, from Carnegie Stage (CS) 17 until 21 weeks post conception (WPC). For most timepoints the study includes two biological replicates for each sex. Additionally, the study includes three technical replicates of a Klinefelter Syndrome (XXY karyotype) testis sample at 13WPC. Human prenatal tissue samples were provided by the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) and obtained from elective terminations of pregnancy. The samples were classified according to a particular Carnegie stage or week post conception based on their external physical appearance and measurements. Single-cell barcoding and library preparation were performed using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).biostudies-arrayexpressLibrary Construction - Nuclei were processed using Chromium Single Cell ATAC Reagent kits (v1) and the Chromium Controller instrument (10x Genomics; RRID:SCR_019326), following the manufacturer's guidelines. The process included tagmentation, single cell barcoding, and library preparation. The libraries were then amplified through 10 PCR cycles and quantified using a Qubit Fluorometer (Thermo Fisher Scientific; RRID:SCR_018095). The average fragment size of the libraries was determined using a Fragment Analyzer (Agilent; RRID:SCR_019417).Sample Collection - Frozen tissue was homogenized on ice in a buffer containing sucrose, KCl, MgCl2, Tris-HCl (pH 8), IGEPAL, DTT, Murine RNase Inhibitor, SUPERase-In, and cOmplete Protease Inhibitor Cocktail. The tissue was disrupted by trituration and/or using a micropestle. After a brief incubation, unlysed tissue debris was removed by low-speed centrifugation (100g for 1 minute at 4°C). The supernatant was then centrifuged at 400g for 4 minutes to separate the nuclei (pellet) from the supernatant. Nuclei were washed once or twice in the homogenization buffer and resuspended in a storage buffer containing sucrose, KCl, MgCl2, Tris-HCl (pH 8), Murine RNase Inhibitor, SUPERase-In, and cOmplete Protease Inhibitor Cocktail. If needed, the nuclei were filtered using 40 µm Flowmi strainers. Nuclei concentration was determined by staining with Hoechst DNA dye or propidium iodide and counting on a Countess II FL Automated Cell Counter. Following the nuclei count, approximately 15,000 nuclei were used for snATAC libraries.Sequencing - Sequencing was performed on a NextSeq 500/550 (Illumina; RRID:SCR_016381) with 34 cycles for both Read 1 and Read 2, 8 cycles for the i7 index, and 16 cycles for the i5 index.Nucleic Acid Extraction - RNA was extracted from the cytoplasm extracts or nuclei suspensions by mixing them with RLT buffer (supplemented with 40 mM DTT) and 100% ethanol in a 2:7:5 ratio. The RNA was then purified using the RNeasy Micro Kit from Qiagen. The quality of the extracted RNA was assessed using a Fragment Analyzer (Advanced Analytical), and all samples had RNA quality numbers (RQN) above 8.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Barcodes corresponding to nuclei were distinguished from empty droplets using ArchR (1.0.2), requiring at least 5,000 fragments and a minimum TSS enrichment of 3. Doublets were removed through an iterative approach. ArchR (1.0.2) was used to generate the LSI embedding, identify peaks in a cluster-specific and replicate-aware manner (also using MACS2 (2.1.2), estimate gene scores and TF motif accessibility scores (also using chromVar 1.20.2).Sequence Alignment - Raw sequencing data were demultiplexed and converted to fastq format using cellranger-atac mkfastq (1.1.0). Cellranger-atac count (1.1.0) was used to correct droplet barcodes for sequencing errors, align reads to the human genome (hg38), generate position-corrected tabular fragment files and identify PCR duplicates from fragments with identical positions originating from the same droplet barcode.UnknownTranscriptomicsGenomicsProteomicsChromium 10xNextSeq 550scATAC-seqHomo sapiensNils Jonathan TrostfalsesnATAC-seq of the developing human female and male gonads across prenatal developmentThis study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 22,032 nuclei in the developing human female and male gonads across several timepoints during prenatal development, from Carnegie Stage (CS) 17 until 21 weeks post conception (WPC). For most timepoints the study includes two biological replicates for each sex. Additionally, the study includes three technical replicates of a Klinefelter Syndrome (XXY karyotype) testis sample at 13WPC. Human prenatal tissue samples were provided by the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) and obtained from elective terminations of pregnancy. The samples were classified according to a particular Carnegie stage or week post conception based on their external physical appearance and measurements. Single-cell barcoding and library preparation were performed using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).2025-06-30T00:00:00Z2025-04-10T16:24:15.526Z2025-04-10T16:24:15.526ZE-MTAB-15028ERP171492E-MTAB-15021E-MTAB-15024E-MTAB-15025EFO_0002944EFO_0004170EFO_0010891EFO_0004917EFO_0005518EFO_0003816EFO_0004184